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          <span data-v-73c95a87>2020 - </span>
          2022
        </a></span></div></div> <div data-v-584a622c><main class="page"><!----> <div class="page-title" style="display:none;"><h1>hifiasm组装</h1> <hr> <div data-v-7b2e794a><i class="iconfont reco-account" data-v-7b2e794a><span data-v-7b2e794a>BioNote</span></i> <i class="iconfont reco-date" data-v-7b2e794a><span data-v-7b2e794a>2020-12-15</span></i> <!----> <i class="iconfont reco-tag tags" data-v-7b2e794a><span class="tag-item" data-v-7b2e794a>
      assembly
    </span><span class="tag-item" data-v-7b2e794a>
      hifiasm
    </span></i></div></div> <div class="theme-reco-content content__default" style="display:none;"><div id="boxx" data-v-e16ac808><div data-v-e16ac808><p v-if="true" class="custom-block-title" data-v-e16ac808></p> <p v-if="true" data-v-e16ac808></p></div></div> <p></p><div class="table-of-contents"><ul><li><a href="#软件安装及测试">软件安装及测试</a><ul><li><a href="#安装方法">安装方法</a></li><li><a href="#小测试数据下载">小测试数据下载</a></li><li><a href="#测试数据运行">测试数据运行</a></li></ul></li><li><a href="#软件参数">软件参数</a></li><li><a href="#trio-binning组装">Trio binning组装</a></li><li><a href="#输出结果">输出结果</a><ul><li><a href="#non-trio-assembly">non-trio assembly</a></li><li><a href="#trio-assembly">trio assembly</a></li></ul></li><li><a href="#组装软件比较">组装软件比较</a></li><li><a href="#其他">其他</a><ul><li><a href="#hifi-组装实例">HiFi 组装实例</a></li><li><a href="#帮助">帮助</a></li></ul></li></ul></div><p></p> <h1 id="介绍"><a href="#介绍" class="header-anchor">#</a> 介绍</h1> <p>Hifiasm 是一款针对PacBio Hifi reads单倍体解析的快速从头组装工具</p> <div class="custom-block tip"><p class="custom-block-title">仓库地址</p> <p>https://github.com/chhylp123/hifiasm <br></p></div> <div class="custom-block tip"><p class="custom-block-title">文章</p> <p>https://arxiv.org/pdf/2008.01237.pdf</p></div> <h2 id="软件安装及测试"><a href="#软件安装及测试" class="header-anchor">#</a> 软件安装及测试</h2> <h3 id="安装方法"><a href="#安装方法" class="header-anchor">#</a> 安装方法</h3> <div class="language-sh line-numbers-mode"><pre class="language-sh"><code><span class="token comment"># Install hifiasm (requiring g++ and zlib)</span>
<span class="token function">git</span> clone https://github.com/chhylp123/hifiasm
<span class="token builtin class-name">cd</span> hifiasm <span class="token operator">&amp;&amp;</span> <span class="token function">make</span>
</code></pre> <div class="line-numbers-wrapper"><span class="line-number">1</span><br><span class="line-number">2</span><br><span class="line-number">3</span><br></div></div><h3 id="小测试数据下载"><a href="#小测试数据下载" class="header-anchor">#</a> 小测试数据下载</h3> <div class="language- line-numbers-mode"><pre class="language-text"><code>wget https://github.com/chhylp123/hifiasm/releases/download/v0.7/chr11-2M.fa.gz
</code></pre> <div class="line-numbers-wrapper"><span class="line-number">1</span><br></div></div><p>大数据：<a href="https://www.ncbi.nlm.nih.gov/sra/?term=SRR11606870" target="_blank" rel="noopener noreferrer">小鼠数据<svg xmlns="http://www.w3.org/2000/svg" aria-hidden="true" x="0px" y="0px" viewBox="0 0 100 100" width="15" height="15" class="icon outbound"><path fill="currentColor" d="M18.8,85.1h56l0,0c2.2,0,4-1.8,4-4v-32h-8v28h-48v-48h28v-8h-32l0,0c-2.2,0-4,1.8-4,4v56C14.8,83.3,16.6,85.1,18.8,85.1z"></path> <polygon fill="currentColor" points="45.7,48.7 51.3,54.3 77.2,28.5 77.2,37.2 85.2,37.2 85.2,14.9 62.8,14.9 62.8,22.9 71.5,22.9"></polygon></svg></a></p> <h3 id="测试数据运行"><a href="#测试数据运行" class="header-anchor">#</a> 测试数据运行</h3> <p>针对小数据使用-f0</p> <div class="language-sh line-numbers-mode"><pre class="language-sh"><code>./hifiasm -o <span class="token builtin class-name">test</span> -t4 -f0 chr11-2M.fa.gz <span class="token operator"><span class="token file-descriptor important">2</span>&gt;</span> test.log
</code></pre> <div class="line-numbers-wrapper"><span class="line-number">1</span><br></div></div><p>从gfa文件获得primary contigs</p> <div class="language-sh line-numbers-mode"><pre class="language-sh"><code><span class="token function">awk</span> <span class="token string">'/^S/{print &quot;&gt;&quot;<span class="token variable">$2</span>;print <span class="token variable">$3</span>}'</span> test.p_ctg.gfa <span class="token operator">&gt;</span> test.p_ctg.fa
</code></pre> <div class="line-numbers-wrapper"><span class="line-number">1</span><br></div></div><h2 id="软件参数"><a href="#软件参数" class="header-anchor">#</a> 软件参数</h2> <ol><li>-l0 ：关掉 duplication purging，对于近交或者纯合基因组，建议加上该参数。</li> <li>-t ：CPU 线程</li> <li>-o ： 输出文件的前缀</li> <li>-z20 : 一些旧的HiFi reads可能会存在短的接头，使用该参数进行修剪</li> <li>-f0 : 对于小基因组，该参数可以关闭起始bloom filter(该步骤会在开始时消耗16G内存)</li> <li>-f38/-f39 : 如果基因组大于人类，建议使用该参数以节省内存</li></ol> <h2 id="trio-binning组装"><a href="#trio-binning组装" class="header-anchor">#</a> Trio binning组装</h2> <p>Trio binning使用来自两个亲本基因组的reads，首先将来自后代的长读段划分为单倍型特异性集。然后将每个单体型独立组装，以完成完整的二倍体重建。</p> <p>Trio binning assembly (requiring https://github.com/lh3/yak)</p> <div class="language-sh line-numbers-mode"><pre class="language-sh"><code>yak count -b37 -t16 -o pat.yak <span class="token operator">&lt;</span><span class="token punctuation">(</span><span class="token function">cat</span> pat_1.fq.gz pat_2.fq.gz<span class="token punctuation">)</span> <span class="token operator">&lt;</span><span class="token punctuation">(</span><span class="token function">cat</span> pat_1.fq.gz pat_2.fq.gz<span class="token punctuation">)</span>
yak count -b37 -t16 -o mat.yak <span class="token operator">&lt;</span><span class="token punctuation">(</span><span class="token function">cat</span> mat_1.fq.gz mat_2.fq.gz<span class="token punctuation">)</span> <span class="token operator">&lt;</span><span class="token punctuation">(</span><span class="token function">cat</span> mat_1.fq.gz mat_2.fq.gz<span class="token punctuation">)</span>
hifiasm -o HG002.asm -t32 -1 pat.yak -2 mat.yak HG002-HiFi.fa.gz
</code></pre> <div class="line-numbers-wrapper"><span class="line-number">1</span><br><span class="line-number">2</span><br><span class="line-number">3</span><br></div></div><h2 id="输出结果"><a href="#输出结果" class="header-anchor">#</a> 输出结果</h2> <h3 id="non-trio-assembly"><a href="#non-trio-assembly" class="header-anchor">#</a> non-trio assembly</h3> <ol><li>Haplotype-resolved raw <a href="http://wgs-assembler.sourceforge.net/wiki/index.php/Celera_Assembler_Terminology" target="_blank" rel="noopener noreferrer">unitig<svg xmlns="http://www.w3.org/2000/svg" aria-hidden="true" x="0px" y="0px" viewBox="0 0 100 100" width="15" height="15" class="icon outbound"><path fill="currentColor" d="M18.8,85.1h56l0,0c2.2,0,4-1.8,4-4v-32h-8v28h-48v-48h28v-8h-32l0,0c-2.2,0-4,1.8-4,4v56C14.8,83.3,16.6,85.1,18.8,85.1z"></path> <polygon fill="currentColor" points="45.7,48.7 51.3,54.3 77.2,28.5 77.2,37.2 85.2,37.2 85.2,14.9 62.8,14.9 62.8,22.9 71.5,22.9"></polygon></svg></a> graph in <a href="https://github.com/pmelsted/GFA-spec/blob/master/GFA-spec.md" target="_blank" rel="noopener noreferrer">GFA<svg xmlns="http://www.w3.org/2000/svg" aria-hidden="true" x="0px" y="0px" viewBox="0 0 100 100" width="15" height="15" class="icon outbound"><path fill="currentColor" d="M18.8,85.1h56l0,0c2.2,0,4-1.8,4-4v-32h-8v28h-48v-48h28v-8h-32l0,0c-2.2,0-4,1.8-4,4v56C14.8,83.3,16.6,85.1,18.8,85.1z"></path> <polygon fill="currentColor" points="45.7,48.7 51.3,54.3 77.2,28.5 77.2,37.2 85.2,37.2 85.2,14.9 62.8,14.9 62.8,22.9 71.5,22.9"></polygon></svg></a> format
(<em>prefix</em>.r_utg.gfa). 保留了所有单倍体信息，包括一些体细胞突变和测序错误。</li> <li>Haplotype-resolved processed unitig graph without small bubbles
(<em>prefix</em>.p_utg.gfa). 相对于raw unitig，去除了图上的小气泡；这些小气泡可能是由于体细胞突变和数据里噪音引起的，不是真正的单倍体信息</li> <li>Primary assembly <a href="http://wgs-assembler.sourceforge.net/wiki/index.php/Celera_Assembler_Terminology" target="_blank" rel="noopener noreferrer">contig<svg xmlns="http://www.w3.org/2000/svg" aria-hidden="true" x="0px" y="0px" viewBox="0 0 100 100" width="15" height="15" class="icon outbound"><path fill="currentColor" d="M18.8,85.1h56l0,0c2.2,0,4-1.8,4-4v-32h-8v28h-48v-48h28v-8h-32l0,0c-2.2,0-4,1.8-4,4v56C14.8,83.3,16.6,85.1,18.8,85.1z"></path> <polygon fill="currentColor" points="45.7,48.7 51.3,54.3 77.2,28.5 77.2,37.2 85.2,37.2 85.2,14.9 62.8,14.9 62.8,22.9 71.5,22.9"></polygon></svg></a> graph (<em>prefix</em>.p_ctg.gfa). 折叠了不同的单倍型。</li> <li>Alternate assembly contig graph (<em>prefix</em>.a_ctg.gfa). This graph consists of all assemblies that
are discarded in primary contig graph.</li></ol> <h3 id="trio-assembly"><a href="#trio-assembly" class="header-anchor">#</a> trio assembly</h3> <ol><li>Haplotype-resolved raw <a href="http://wgs-assembler.sourceforge.net/wiki/index.php/Celera_Assembler_Terminology" target="_blank" rel="noopener noreferrer">unitig<svg xmlns="http://www.w3.org/2000/svg" aria-hidden="true" x="0px" y="0px" viewBox="0 0 100 100" width="15" height="15" class="icon outbound"><path fill="currentColor" d="M18.8,85.1h56l0,0c2.2,0,4-1.8,4-4v-32h-8v28h-48v-48h28v-8h-32l0,0c-2.2,0-4,1.8-4,4v56C14.8,83.3,16.6,85.1,18.8,85.1z"></path> <polygon fill="currentColor" points="45.7,48.7 51.3,54.3 77.2,28.5 77.2,37.2 85.2,37.2 85.2,14.9 62.8,14.9 62.8,22.9 71.5,22.9"></polygon></svg></a> graph in <a href="https://github.com/pmelsted/GFA-spec/blob/master/GFA-spec.md" target="_blank" rel="noopener noreferrer">GFA<svg xmlns="http://www.w3.org/2000/svg" aria-hidden="true" x="0px" y="0px" viewBox="0 0 100 100" width="15" height="15" class="icon outbound"><path fill="currentColor" d="M18.8,85.1h56l0,0c2.2,0,4-1.8,4-4v-32h-8v28h-48v-48h28v-8h-32l0,0c-2.2,0-4,1.8-4,4v56C14.8,83.3,16.6,85.1,18.8,85.1z"></path> <polygon fill="currentColor" points="45.7,48.7 51.3,54.3 77.2,28.5 77.2,37.2 85.2,37.2 85.2,14.9 62.8,14.9 62.8,22.9 71.5,22.9"></polygon></svg></a> format
(<em>prefix</em>.r_utg.gfa). This graph keeps all haplotype information.</li> <li>Phased paternal/haplotype1 contig graph (<em>prefix</em>.hap1.p_ctg.gfa). This graph keeps the phased
paternal/haplotype1 assembly.</li> <li>Phased maternal/haplotype2 contig graph (<em>prefix</em>.hap2.p_ctg.gfa). This graph keeps the phased
maternal/haplotype2 assembly.</li></ol> <p>Hifiasm writes error corrected reads to the <em>prefix</em>.ec.bin binary file and
writes overlaps to <em>prefix</em>.ovlp.source.bin and <em>prefix</em>.ovlp.reverse.bin.</p> <div class="custom-block warning"><p>Purging haplotig duplications may introduce misassemblies.</p></div> <h2 id="组装软件比较"><a href="#组装软件比较" class="header-anchor">#</a> 组装软件比较</h2> <p><img src="/img/assembly/stat.png" alt="avatar"></p> <h2 id="其他"><a href="#其他" class="header-anchor">#</a> 其他</h2> <h3 id="hifi-组装实例"><a href="#hifi-组装实例" class="header-anchor">#</a> HiFi 组装实例</h3> <p>The following table shows the statistics of several hifiasm primary assemblies:</p> <table><thead><tr><th style="text-align:left;"><sub>Dataset<sub></sub></sub></th> <th style="text-align:right;"><sub>Size<sub></sub></sub></th> <th style="text-align:right;"><sub>Cov.<sub></sub></sub></th> <th style="text-align:left;"><sub>Asm options<sub></sub></sub></th> <th style="text-align:right;"><sub>CPU time<sub></sub></sub></th> <th style="text-align:right;"><sub>Wall time<sub></sub></sub></th> <th style="text-align:right;"><sub>RAM<sub></sub></sub></th> <th style="text-align:right;"><sub> N50<sub></sub></sub></th></tr></thead> <tbody><tr><td style="text-align:left;"><sub><a href="https://www.ncbi.nlm.nih.gov/sra/?term=SRR11606870" target="_blank" rel="noopener noreferrer">Mouse (C57/BL6J)<svg xmlns="http://www.w3.org/2000/svg" aria-hidden="true" x="0px" y="0px" viewBox="0 0 100 100" width="15" height="15" class="icon outbound"><path fill="currentColor" d="M18.8,85.1h56l0,0c2.2,0,4-1.8,4-4v-32h-8v28h-48v-48h28v-8h-32l0,0c-2.2,0-4,1.8-4,4v56C14.8,83.3,16.6,85.1,18.8,85.1z"></path> <polygon fill="currentColor" points="45.7,48.7 51.3,54.3 77.2,28.5 77.2,37.2 85.2,37.2 85.2,14.9 62.8,14.9 62.8,22.9 71.5,22.9"></polygon></svg></a></sub></td> <td style="text-align:right;"><sub>2.6Gb</sub></td> <td style="text-align:right;"><sub>×25</sub></td> <td style="text-align:left;"><sub>-t48 -l0</sub></td> <td style="text-align:right;"><sub>172.9h</sub></td> <td style="text-align:right;"><sub>4.8h</sub></td> <td style="text-align:right;"><sub>76G</sub></td> <td style="text-align:right;"><sub>21.1Mb</sub></td></tr> <tr><td style="text-align:left;"><sub><a href="https://www.ncbi.nlm.nih.gov/sra/?term=SRR11606869" target="_blank" rel="noopener noreferrer">Maize (B73)<svg xmlns="http://www.w3.org/2000/svg" aria-hidden="true" x="0px" y="0px" viewBox="0 0 100 100" width="15" height="15" class="icon outbound"><path fill="currentColor" d="M18.8,85.1h56l0,0c2.2,0,4-1.8,4-4v-32h-8v28h-48v-48h28v-8h-32l0,0c-2.2,0-4,1.8-4,4v56C14.8,83.3,16.6,85.1,18.8,85.1z"></path> <polygon fill="currentColor" points="45.7,48.7 51.3,54.3 77.2,28.5 77.2,37.2 85.2,37.2 85.2,14.9 62.8,14.9 62.8,22.9 71.5,22.9"></polygon></svg></a></sub></td> <td style="text-align:right;"><sub>2.2Gb</sub></td> <td style="text-align:right;"><sub>×22</sub></td> <td style="text-align:left;"><sub>-t48 -l0</sub></td> <td style="text-align:right;"><sub>203.2h</sub></td> <td style="text-align:right;"><sub>5.1h</sub></td> <td style="text-align:right;"><sub>68G</sub></td> <td style="text-align:right;"><sub>36.7Mb</sub></td></tr> <tr><td style="text-align:left;"><sub><a href="https://www.ncbi.nlm.nih.gov/sra/?term=SRR11606867" target="_blank" rel="noopener noreferrer">Strawberry<svg xmlns="http://www.w3.org/2000/svg" aria-hidden="true" x="0px" y="0px" viewBox="0 0 100 100" width="15" height="15" class="icon outbound"><path fill="currentColor" d="M18.8,85.1h56l0,0c2.2,0,4-1.8,4-4v-32h-8v28h-48v-48h28v-8h-32l0,0c-2.2,0-4,1.8-4,4v56C14.8,83.3,16.6,85.1,18.8,85.1z"></path> <polygon fill="currentColor" points="45.7,48.7 51.3,54.3 77.2,28.5 77.2,37.2 85.2,37.2 85.2,14.9 62.8,14.9 62.8,22.9 71.5,22.9"></polygon></svg></a></sub></td> <td style="text-align:right;"><sub>0.8Gb</sub></td> <td style="text-align:right;"><sub>×36</sub></td> <td style="text-align:left;"><sub>-t48 -D10</sub></td> <td style="text-align:right;"><sub>152.7h</sub></td> <td style="text-align:right;"><sub>3.7h</sub></td> <td style="text-align:right;"><sub>91G</sub></td> <td style="text-align:right;"><sub>17.8Mb</sub></td></tr> <tr><td style="text-align:left;"><sub><a href="https://www.ncbi.nlm.nih.gov/sra?term=(SRR11606868)%20OR%20SRR12048570" target="_blank" rel="noopener noreferrer">Frog<svg xmlns="http://www.w3.org/2000/svg" aria-hidden="true" x="0px" y="0px" viewBox="0 0 100 100" width="15" height="15" class="icon outbound"><path fill="currentColor" d="M18.8,85.1h56l0,0c2.2,0,4-1.8,4-4v-32h-8v28h-48v-48h28v-8h-32l0,0c-2.2,0-4,1.8-4,4v56C14.8,83.3,16.6,85.1,18.8,85.1z"></path> <polygon fill="currentColor" points="45.7,48.7 51.3,54.3 77.2,28.5 77.2,37.2 85.2,37.2 85.2,14.9 62.8,14.9 62.8,22.9 71.5,22.9"></polygon></svg></a></sub></td> <td style="text-align:right;"><sub>9.5Gb</sub></td> <td style="text-align:right;"><sub>×29</sub></td> <td style="text-align:left;"><sub>-t48</sub></td> <td style="text-align:right;"><sub>2834.3h</sub></td> <td style="text-align:right;"><sub>69.0h</sub></td> <td style="text-align:right;"><sub>463G</sub></td> <td style="text-align:right;"><sub>9.3Mb</sub></td></tr> <tr><td style="text-align:left;"><sub><a href="https://www.ncbi.nlm.nih.gov/sra/?term=SRP251156" target="_blank" rel="noopener noreferrer">Redwood<svg xmlns="http://www.w3.org/2000/svg" aria-hidden="true" x="0px" y="0px" viewBox="0 0 100 100" width="15" height="15" class="icon outbound"><path fill="currentColor" d="M18.8,85.1h56l0,0c2.2,0,4-1.8,4-4v-32h-8v28h-48v-48h28v-8h-32l0,0c-2.2,0-4,1.8-4,4v56C14.8,83.3,16.6,85.1,18.8,85.1z"></path> <polygon fill="currentColor" points="45.7,48.7 51.3,54.3 77.2,28.5 77.2,37.2 85.2,37.2 85.2,14.9 62.8,14.9 62.8,22.9 71.5,22.9"></polygon></svg></a></sub></td> <td style="text-align:right;"><sub>35.6Gb</sub></td> <td style="text-align:right;"><sub>×28</sub></td> <td style="text-align:left;"><sub>-t80</sub></td> <td style="text-align:right;"><sub>3890.3h</sub></td> <td style="text-align:right;"><sub>65.5h</sub></td> <td style="text-align:right;"><sub>699G</sub></td> <td style="text-align:right;"><sub>5.4Mb</sub></td></tr> <tr><td style="text-align:left;"><sub><a href="https://www.ncbi.nlm.nih.gov/sra?term=(((SRR11292120)%20OR%20SRR11292121)%20OR%20SRR11292122)%20OR%20SRR11292123" target="_blank" rel="noopener noreferrer">Human (CHM13)<svg xmlns="http://www.w3.org/2000/svg" aria-hidden="true" x="0px" y="0px" viewBox="0 0 100 100" width="15" height="15" class="icon outbound"><path fill="currentColor" d="M18.8,85.1h56l0,0c2.2,0,4-1.8,4-4v-32h-8v28h-48v-48h28v-8h-32l0,0c-2.2,0-4,1.8-4,4v56C14.8,83.3,16.6,85.1,18.8,85.1z"></path> <polygon fill="currentColor" points="45.7,48.7 51.3,54.3 77.2,28.5 77.2,37.2 85.2,37.2 85.2,14.9 62.8,14.9 62.8,22.9 71.5,22.9"></polygon></svg></a></sub></td> <td style="text-align:right;"><sub>3.1Gb</sub></td> <td style="text-align:right;"><sub>×32</sub></td> <td style="text-align:left;"><sub>-t48 -l0</sub></td> <td style="text-align:right;"><sub>310.7h</sub></td> <td style="text-align:right;"><sub>8.2h</sub></td> <td style="text-align:right;"><sub>114G</sub></td> <td style="text-align:right;"><sub>88.9Mb</sub></td></tr> <tr><td style="text-align:left;"><sub><a href="https://www.ebi.ac.uk/ena/data/view/ERX3831682" target="_blank" rel="noopener noreferrer">Human (HG00733)<svg xmlns="http://www.w3.org/2000/svg" aria-hidden="true" x="0px" y="0px" viewBox="0 0 100 100" width="15" height="15" class="icon outbound"><path fill="currentColor" d="M18.8,85.1h56l0,0c2.2,0,4-1.8,4-4v-32h-8v28h-48v-48h28v-8h-32l0,0c-2.2,0-4,1.8-4,4v56C14.8,83.3,16.6,85.1,18.8,85.1z"></path> <polygon fill="currentColor" points="45.7,48.7 51.3,54.3 77.2,28.5 77.2,37.2 85.2,37.2 85.2,14.9 62.8,14.9 62.8,22.9 71.5,22.9"></polygon></svg></a></sub></td> <td style="text-align:right;"><sub>3.1Gb</sub></td> <td style="text-align:right;"><sub>×33</sub></td> <td style="text-align:left;"><sub>-t48</sub></td> <td style="text-align:right;"><sub>269.1h</sub></td> <td style="text-align:right;"><sub>6.9h</sub></td> <td style="text-align:right;"><sub>135G</sub></td> <td style="text-align:right;"><sub>69.9Mb</sub></td></tr> <tr><td style="text-align:left;"><sub><a href="https://www.ncbi.nlm.nih.gov/sra?term=(((SRR10382244)%20OR%20SRR10382245)%20OR%20SRR10382248)%20OR%20SRR10382249" target="_blank" rel="noopener noreferrer">Human (HG002)<svg xmlns="http://www.w3.org/2000/svg" aria-hidden="true" x="0px" y="0px" viewBox="0 0 100 100" width="15" height="15" class="icon outbound"><path fill="currentColor" d="M18.8,85.1h56l0,0c2.2,0,4-1.8,4-4v-32h-8v28h-48v-48h28v-8h-32l0,0c-2.2,0-4,1.8-4,4v56C14.8,83.3,16.6,85.1,18.8,85.1z"></path> <polygon fill="currentColor" points="45.7,48.7 51.3,54.3 77.2,28.5 77.2,37.2 85.2,37.2 85.2,14.9 62.8,14.9 62.8,22.9 71.5,22.9"></polygon></svg></a></sub></td> <td style="text-align:right;"><sub>3.1Gb</sub></td> <td style="text-align:right;"><sub>×36</sub></td> <td style="text-align:left;"><sub>-t48</sub></td> <td style="text-align:right;"><sub>305.4h</sub></td> <td style="text-align:right;"><sub>7.7h</sub></td> <td style="text-align:right;"><sub>137G</sub></td> <td style="text-align:right;"><sub>98.7Mb</sub></td></tr></tbody></table> <p>Hifiasm can assemble a 3.1Gb human genome in several hours or a ~30Gb hexaploid
redwood genome in a few days on a single machine. For trio binning assembly:</p> <table><thead><tr><th style="text-align:left;"><sub>Dataset<sub></sub></sub></th> <th style="text-align:right;"><sub>Cov.<sub></sub></sub></th> <th style="text-align:right;"><sub>CPU time<sub></sub></sub></th> <th style="text-align:right;"><sub>Elapsed time<sub></sub></sub></th> <th style="text-align:right;"><sub>RAM<sub></sub></sub></th> <th style="text-align:right;"><sub> N50<sub></sub></sub></th></tr></thead> <tbody><tr><td style="text-align:left;"><sub><a href="https://www.ebi.ac.uk/ena/data/view/ERX3831682" target="_blank" rel="noopener noreferrer">HG00733<svg xmlns="http://www.w3.org/2000/svg" aria-hidden="true" x="0px" y="0px" viewBox="0 0 100 100" width="15" height="15" class="icon outbound"><path fill="currentColor" d="M18.8,85.1h56l0,0c2.2,0,4-1.8,4-4v-32h-8v28h-48v-48h28v-8h-32l0,0c-2.2,0-4,1.8-4,4v56C14.8,83.3,16.6,85.1,18.8,85.1z"></path> <polygon fill="currentColor" points="45.7,48.7 51.3,54.3 77.2,28.5 77.2,37.2 85.2,37.2 85.2,14.9 62.8,14.9 62.8,22.9 71.5,22.9"></polygon></svg></a>, <a href="https://www.ebi.ac.uk/ena/data/view/ERR3241754" target="_blank" rel="noopener noreferrer">[father]<svg xmlns="http://www.w3.org/2000/svg" aria-hidden="true" x="0px" y="0px" viewBox="0 0 100 100" width="15" height="15" class="icon outbound"><path fill="currentColor" d="M18.8,85.1h56l0,0c2.2,0,4-1.8,4-4v-32h-8v28h-48v-48h28v-8h-32l0,0c-2.2,0-4,1.8-4,4v56C14.8,83.3,16.6,85.1,18.8,85.1z"></path> <polygon fill="currentColor" points="45.7,48.7 51.3,54.3 77.2,28.5 77.2,37.2 85.2,37.2 85.2,14.9 62.8,14.9 62.8,22.9 71.5,22.9"></polygon></svg></a>, <a href="https://www.ebi.ac.uk/ena/data/view/ERR3241755" target="_blank" rel="noopener noreferrer">[mother]<svg xmlns="http://www.w3.org/2000/svg" aria-hidden="true" x="0px" y="0px" viewBox="0 0 100 100" width="15" height="15" class="icon outbound"><path fill="currentColor" d="M18.8,85.1h56l0,0c2.2,0,4-1.8,4-4v-32h-8v28h-48v-48h28v-8h-32l0,0c-2.2,0-4,1.8-4,4v56C14.8,83.3,16.6,85.1,18.8,85.1z"></path> <polygon fill="currentColor" points="45.7,48.7 51.3,54.3 77.2,28.5 77.2,37.2 85.2,37.2 85.2,14.9 62.8,14.9 62.8,22.9 71.5,22.9"></polygon></svg></a></sub></td> <td style="text-align:right;"><sub>×33</sub></td> <td style="text-align:right;"><sub>269.1h</sub></td> <td style="text-align:right;"><sub>6.9h</sub></td> <td style="text-align:right;"><sub>135G</sub></td> <td style="text-align:right;"><sub>35.1Mb (paternal), 34.9Mb (maternal)</sub></td></tr> <tr><td style="text-align:left;"><sub><a href="https://www.ncbi.nlm.nih.gov/sra?term=(((SRR10382244)%20OR%20SRR10382245)%20OR%20SRR10382248)%20OR%20SRR10382249" target="_blank" rel="noopener noreferrer">HG002<svg xmlns="http://www.w3.org/2000/svg" aria-hidden="true" x="0px" y="0px" viewBox="0 0 100 100" width="15" height="15" class="icon outbound"><path fill="currentColor" d="M18.8,85.1h56l0,0c2.2,0,4-1.8,4-4v-32h-8v28h-48v-48h28v-8h-32l0,0c-2.2,0-4,1.8-4,4v56C14.8,83.3,16.6,85.1,18.8,85.1z"></path> <polygon fill="currentColor" points="45.7,48.7 51.3,54.3 77.2,28.5 77.2,37.2 85.2,37.2 85.2,14.9 62.8,14.9 62.8,22.9 71.5,22.9"></polygon></svg></a>,   <a href="https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/HG003_NA24149_father/NIST_HiSeq_HG003_Homogeneity-12389378/HG003Run01-13262252/" target="_blank" rel="noopener noreferrer">[father]<svg xmlns="http://www.w3.org/2000/svg" aria-hidden="true" x="0px" y="0px" viewBox="0 0 100 100" width="15" height="15" class="icon outbound"><path fill="currentColor" d="M18.8,85.1h56l0,0c2.2,0,4-1.8,4-4v-32h-8v28h-48v-48h28v-8h-32l0,0c-2.2,0-4,1.8-4,4v56C14.8,83.3,16.6,85.1,18.8,85.1z"></path> <polygon fill="currentColor" points="45.7,48.7 51.3,54.3 77.2,28.5 77.2,37.2 85.2,37.2 85.2,14.9 62.8,14.9 62.8,22.9 71.5,22.9"></polygon></svg></a>, <a href="https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/HG004_NA24143_mother/NIST_HiSeq_HG004_Homogeneity-14572558/HG004Run01-15133132/" target="_blank" rel="noopener noreferrer">[mother]<svg xmlns="http://www.w3.org/2000/svg" aria-hidden="true" x="0px" y="0px" viewBox="0 0 100 100" width="15" height="15" class="icon outbound"><path fill="currentColor" d="M18.8,85.1h56l0,0c2.2,0,4-1.8,4-4v-32h-8v28h-48v-48h28v-8h-32l0,0c-2.2,0-4,1.8-4,4v56C14.8,83.3,16.6,85.1,18.8,85.1z"></path> <polygon fill="currentColor" points="45.7,48.7 51.3,54.3 77.2,28.5 77.2,37.2 85.2,37.2 85.2,14.9 62.8,14.9 62.8,22.9 71.5,22.9"></polygon></svg></a></sub></td> <td style="text-align:right;"><sub>×36</sub></td> <td style="text-align:right;"><sub>305.4h</sub></td> <td style="text-align:right;"><sub>7.7h</sub></td> <td style="text-align:right;"><sub>137G</sub></td> <td style="text-align:right;"><sub>41.0Mb (paternal), 40.8Mb (maternal)</sub></td></tr> <tr><td style="text-align:left;"><sub><a href="https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/NA12878/PacBio_SequelII_CCS_11kb/" target="_blank" rel="noopener noreferrer">NA12878<svg xmlns="http://www.w3.org/2000/svg" aria-hidden="true" x="0px" y="0px" viewBox="0 0 100 100" width="15" height="15" class="icon outbound"><path fill="currentColor" d="M18.8,85.1h56l0,0c2.2,0,4-1.8,4-4v-32h-8v28h-48v-48h28v-8h-32l0,0c-2.2,0-4,1.8-4,4v56C14.8,83.3,16.6,85.1,18.8,85.1z"></path> <polygon fill="currentColor" points="45.7,48.7 51.3,54.3 77.2,28.5 77.2,37.2 85.2,37.2 85.2,14.9 62.8,14.9 62.8,22.9 71.5,22.9"></polygon></svg></a>, <a href="https://www.ebi.ac.uk/ena/data/view/ERR194160" target="_blank" rel="noopener noreferrer">[father]<svg xmlns="http://www.w3.org/2000/svg" aria-hidden="true" x="0px" y="0px" viewBox="0 0 100 100" width="15" height="15" class="icon outbound"><path fill="currentColor" d="M18.8,85.1h56l0,0c2.2,0,4-1.8,4-4v-32h-8v28h-48v-48h28v-8h-32l0,0c-2.2,0-4,1.8-4,4v56C14.8,83.3,16.6,85.1,18.8,85.1z"></path> <polygon fill="currentColor" points="45.7,48.7 51.3,54.3 77.2,28.5 77.2,37.2 85.2,37.2 85.2,14.9 62.8,14.9 62.8,22.9 71.5,22.9"></polygon></svg></a>, <a href="https://www.ebi.ac.uk/ena/data/view/ERR194161" target="_blank" rel="noopener noreferrer">[mother]<svg xmlns="http://www.w3.org/2000/svg" aria-hidden="true" x="0px" y="0px" viewBox="0 0 100 100" width="15" height="15" class="icon outbound"><path fill="currentColor" d="M18.8,85.1h56l0,0c2.2,0,4-1.8,4-4v-32h-8v28h-48v-48h28v-8h-32l0,0c-2.2,0-4,1.8-4,4v56C14.8,83.3,16.6,85.1,18.8,85.1z"></path> <polygon fill="currentColor" points="45.7,48.7 51.3,54.3 77.2,28.5 77.2,37.2 85.2,37.2 85.2,14.9 62.8,14.9 62.8,22.9 71.5,22.9"></polygon></svg></a></sub></td> <td style="text-align:right;"><sub>×30</sub></td> <td style="text-align:right;"><sub>180.8h</sub></td> <td style="text-align:right;"><sub>4.9h</sub></td> <td style="text-align:right;"><sub>123G</sub></td> <td style="text-align:right;"><sub>27.7Mb (paternal), 27.0Mb (maternal)</sub></td></tr></tbody></table> <p>Except NA12878, the assemblies above were produced by hifiasm v0.12 and can be
downloaded at</p> <div class="language-txt line-numbers-mode"><pre class="language-text"><code>ftp://ftp.dfci.harvard.edu/pub/hli/hifiasm/submission/hifiasm-0.12/
</code></pre> <div class="line-numbers-wrapper"><span class="line-number">1</span><br></div></div><p>NA12878 was assembled with an older version of hifiasm and is available at</p> <div class="language-txt line-numbers-mode"><pre class="language-text"><code>ftp://ftp.dfci.harvard.edu/pub/hli/hifiasm/NA12878-r253/
</code></pre> <div class="line-numbers-wrapper"><span class="line-number">1</span><br></div></div><h3 id="帮助"><a href="#帮助" class="header-anchor">#</a> 帮助</h3> <p>For detailed description of options, please see <code>man ./hifiasm.1</code>. The <code>-h</code>
option of hifiasm also provides brief description of options. If you have
further questions, please raise an issue at the <a href="https://github.com/chhylp123/hifiasm/issues" target="_blank" rel="noopener noreferrer">issue
page<svg xmlns="http://www.w3.org/2000/svg" aria-hidden="true" x="0px" y="0px" viewBox="0 0 100 100" width="15" height="15" class="icon outbound"><path fill="currentColor" d="M18.8,85.1h56l0,0c2.2,0,4-1.8,4-4v-32h-8v28h-48v-48h28v-8h-32l0,0c-2.2,0-4,1.8-4,4v56C14.8,83.3,16.6,85.1,18.8,85.1z"></path> <polygon fill="currentColor" points="45.7,48.7 51.3,54.3 77.2,28.5 77.2,37.2 85.2,37.2 85.2,14.9 62.8,14.9 62.8,22.9 71.5,22.9"></polygon></svg></a>.</p></div> <footer class="page-edit" style="display:none;"><!----> <!----></footer> <!----> <!----> <div class="article-list" data-v-2af88190><div class="article-title" data-v-2af88190><a href="/timeline/" class="iconfont icon-shizhong" data-v-2af88190>最近更新</a></div> <div class="article-wrapper" data-v-2af88190><dl data-v-2af88190><dd data-v-2af88190>01</dd> <dt data-v-2af88190><a href="/views/software/busco.html" data-v-2af88190><div data-v-2af88190>BUSCO v5</div></a> <span data-v-2af88190>03-01</span></dt></dl><dl data-v-2af88190><dd data-v-2af88190>02</dd> <dt data-v-2af88190><a href="/views/software/peregrine.html" data-v-2af88190><div data-v-2af88190>Peregrine组装</div></a> <span data-v-2af88190>12-16</span></dt></dl><dl data-v-2af88190><dd data-v-2af88190>03</dd> <dt data-v-2af88190><a href="/views/nextflow/install.html" data-v-2af88190><div data-v-2af88190>nextflow安装</div></a> <span data-v-2af88190>09-07</span></dt></dl></div> <div data-v-2af88190><a href="/timeline/" class="article-more" data-v-2af88190>更多文章 &gt;</a></div></div></main> <!----> <div class="comments-wrapper" style="display:none;" data-v-584a622c><!----></div></div></div></div></div></div><div class="global-ui"><div class="back-to-ceiling" style="right:1rem;bottom:6rem;width:2.5rem;height:2.5rem;border-radius:.25rem;line-height:2.5rem;display:none;" data-v-a81d141e data-v-a81d141e><svg t="1574745035067" viewBox="0 0 1024 1024" version="1.1" xmlns="http://www.w3.org/2000/svg" p-id="5404" class="icon" data-v-a81d141e><path d="M526.60727968 10.90185116a27.675 27.675 0 0 0-29.21455937 0c-131.36607665 82.28402758-218.69155461 228.01873535-218.69155402 394.07834331a462.20625001 462.20625001 0 0 0 5.36959153 69.94390903c1.00431239 6.55289093-0.34802892 13.13561351-3.76865779 18.80351572-32.63518765 54.11355614-51.75690182 118.55860487-51.7569018 187.94566865a371.06718723 371.06718723 0 0 0 11.50484808 91.98906777c6.53300375 25.50556257 41.68394495 28.14064038 52.69160883 4.22606766 17.37162448-37.73630017 42.14135425-72.50938081 72.80769204-103.21549295 2.18761121 3.04276886 4.15646224 6.24463696 6.40373557 9.22774369a1871.4375 1871.4375 0 0 0 140.04691725 5.34970492 1866.36093723 1866.36093723 0 0 0 140.04691723-5.34970492c2.24727335-2.98310674 4.21612437-6.18497483 6.3937923-9.2178004 30.66633723 30.70611158 55.4360664 65.4791928 72.80769147 103.21549355 11.00766384 23.91457269 46.15860503 21.27949489 52.69160879-4.22606768a371.15156223 371.15156223 0 0 0 11.514792-91.99901164c0-69.36717486-19.13165746-133.82216804-51.75690182-187.92578088-3.42062944-5.66790279-4.76302748-12.26056868-3.76865837-18.80351632a462.20625001 462.20625001 0 0 0 5.36959269-69.943909c-0.00994388-166.08943902-87.32547796-311.81420293-218.6915546-394.09823051zM605.93803103 357.87693858a93.93749974 93.93749974 0 1 1-187.89594924 6.1e-7 93.93749974 93.93749974 0 0 1 187.89594924-6.1e-7z" p-id="5405" data-v-a81d141e></path><path d="M429.50777625 765.63860547C429.50777625 803.39355007 466.44236686 1000.39046097 512.00932183 1000.39046097c45.56695499 0 82.4922232-197.00623328 82.5015456-234.7518555 0-37.75494459-36.9345906-68.35043303-82.4922232-68.34111062-45.57627738-0.00932239-82.52019037 30.59548842-82.51086798 68.34111062z" p-id="5406" data-v-a81d141e></path></svg></div><!----><div data-v-48108b4c><div class="DetailsOpenFlag" style="right:1rem;bottom:9rem;width:2.5rem;height:2.5rem;border-radius:.25rem;line-height:2.5rem;font-size:14px;font-weight:500;display:none;" data-v-48108b4c>
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